VMD-L Mailing List

From: Philippe Bopp (philippebopp_at_REMOVE_yahoo.com)
Date: Sat Nov 27 2021 - 17:32:46 CST

      hi

     Axel wrote:

>people don't understand what you have been asking, either because you have not explained it well enough or >because they got confused about your use of the english language
>
>people think that you could easily resolve you problem on your own, e.g. by checking the documentation more >thoroughly

 it is a combination of both, I suppose, but since you are an undergrad,
 let me try some linguistic guesses for didactic purposes

 
>> How can I construct exact same coordination

 How can I construct myself the atom coordinates that VMD ('s plugin) constructs

    see https://www.ks.uiuc.edu/Research/vmd/plugins/nanotube/
    which tells you everything you need to know if you want to code it yourself

>of atoms box

    box? if you want to use periodic boundary conditions (pbc), you will have
    to decide yourself what they should be

>in the CNT data file which is developed by VMD?

  if you want to have a 'data file',
  see the VMD save option:
   File -> save coordinates 
        select atoms all
        the file format you want (many choices)

  Philippe

-----------------
Philippe A. Bopp
professor of chemistry (retired)

philippebopp  AT yahoo.com
--------------- 

>> lattice_box = (80.5*80.5*161) angstrom
>> Chirality(n,m) = (10,10)
>> Diameter= 1.3751 nm
>> length = 7.8566 nm
>>
>>  #  generated by VMD         1280  atoms           1  atom types       0.000000000000      80.5000000  xlo xhi (?????)      0.000000000000      80.5000000  ylo yhi (?????)      0.000000000000      161.000000  zlo zhi (?????) Masses             1   12.01100000             # C Atoms # atomic
>>          1    1       47.125494            40.250000             41.217088
>>          2    1      46.975248            41.679496              41.217088
>>          3    1      45.812391            44.291314              41.217088 
>>
>>
>>
>> I got the data.
>>
>>  #  generated by VMD
>>  
>>         1280  atoms
>>            1  atom types
>>  
>>       0.000000000000      15.559482000000  xlo xhi
>>       0.000000000000      15.559482000000  ylo yhi
>>       0.000000000000      79.365517000000  zlo zhi
>>  
>> Masses
>>  
>>             1   12.01100000             # C
>>  
>> Atoms # atomic
>>  
>>          1    1        6.779741000000       0.000000000000       0.000000000000
>>          2    1        6.631588000000       1.409587000000       0.000000000000
>>          3    1        6.447917000000       2.095055000000       1.228024000000  (wrong coordination)
>>
>> Please help me. Your small help will be fruitful for me.
>>
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!srBRoWPDDa-KmJ7Q-pTcwvZzTQXmdCjBaBK7Dsly-oDr8IsldB4nYMiqsHH1zd7Q1w$ 
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.